changeset 2:73263d5c2c9f

Remove botched upload (see Galaxy issue 586)
author g2cmnty@test-web1.g2.bx.psu.edu
date Tue, 21 Jun 2011 09:48:11 -0400
parents e53a79816f5f
children 298f5c1d9521
files mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.py mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.txt mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.xml
diffstat 3 files changed, 0 insertions(+), 316 deletions(-) [+]
line wrap: on
line diff
--- a/mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.py	Thu Jun 16 04:44:00 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-#!/usr/bin/env python
-"""A simple wrapper script to call MIRA and collect its output.
-"""
-import os
-import sys
-import subprocess
-import shutil
-import time
-
-def stop_err(msg, err=1):
-    sys.stderr.write(msg+"\n")
-    sys.exit(err)
-
-def tcs_to_tabular(old, new):
-    in_handle = open(old, "rU")
-    out_handle = open(new, "w")
-    assert in_handle.readline() == "#TCS V1.0\n"
-    assert in_handle.readline() == "#\n"
-    assert in_handle.readline() == "# contig name          padPos  upadPos | B  Q | tcov covA covC covG covT cov* | qA qC qG qT q* |  S | Tags\n"
-    assert in_handle.readline() == "#\n"
-    out_handle.write("#%s\n" % "\t".join(["contig", "pasPos", "upadPos", "B", "Q",
-                                         "tcov", "covA", "covC", "covG", "covT", "cov*",
-                                         "qA", "qC", "qG", "qT", "q*", "S", "Tags"]))
-    for line in in_handle:
-        parts = line.rstrip("\n").split(None,22)
-        assert parts[3] == parts[6] == parts[13] == parts[19] == parts[21] == "|"
-        wanted = parts[:3] + parts[4:6]+parts[7:13]+parts[14:19]+parts[20:21]+parts[22:]
-        out_handle.write("%s\n" % "\t".join(wanted))
-    out_handle.close()
-    in_handle.close()
-
-def collect_output(temp, name):
-    n3 = (temp, name, name, name)
-    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
-    if not os.path.isdir(f):
-        stop_err("Missing output folder")
-    if not os.listdir(f):
-        stop_err("Empty output folder")
-    for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
-                     ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
-                     ("%s/%s_out.wig" % (f, name), out_wig),
-                     ("%s/%s_out.caf" % (f, name), out_caf),
-                     ("%s/%s_out.ace" % (f, name), out_ace)]:
-        if not os.path.isfile(old):
-            stop_err("Missing %s output file" % os.path.splitext(old)[-1])
-        else:
-            shutil.move(old, new)
-    tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs)
-
-def clean_up(temp, name):
-    folder = "%s/%s_assembly" % (temp, name)
-    if os.path.isdir(folder):
-        shutil.rmtree(folder)
-
-#TODO - Run MIRA in /tmp or a configurable directory?
-#Currently Galaxy puts us somewhere safe like:
-#/opt/galaxy-dist/database/job_working_directory/846/
-temp = "."
-name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9]
-
-start_time = time.time()
-cmd = " ".join(sys.argv[9:])
-
-assert os.path.isdir(temp)
-d = "%s_assembly" % name
-assert not os.path.isdir(d)
-try:
-    #Check path access
-    os.mkdir(d)
-except Exception, err:
-    sys.stderr.write("Error making directory %s\n%s" % (d, err))
-    sys.exit(1)
-
-#print os.path.abspath(".")
-#print cmd
-
-handle = open(out_log, "w")
-try:
-    #Run MIRA
-    child = subprocess.Popen(sys.argv[9:],
-                             stdout=handle,
-                             stderr=subprocess.STDOUT)
-except Exception, err:
-    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
-    #TODO - call clean up?
-    handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
-    handle.close()
-    sys.exit(1)
-#Use .communicate as can get deadlocks with .wait(),
-stdout, stderr = child.communicate()
-assert not stdout and not stderr #Should be empty as sent to handle
-run_time = time.time() - start_time
-return_code = child.returncode
-handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
-print "MIRA took %0.2f minutes" % (run_time / 60.0)
-if return_code:
-    handle.write("Return error code %i from command:\n" % return_code)
-    handle.write(cmd + "\n")
-    handle.close()
-    clean_up(temp, name)
-    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
-             return_code)
-handle.close()
-
-collect_output(temp, name)
-clean_up(temp, name)
-print "Done"
--- a/mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.txt	Thu Jun 16 04:44:00 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-Galaxy tool to wrap the MIRA sequence assembly program
-======================================================
-
-This tool is copyright 2011 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (to collect the MIRA output and move it
-to where Galaxy expects the files, and convert MIRA's TCS file into a tab
-separate file for use in Galaxy). There are just two files to install:
-
-* mira.py (the Python script)
-* mira.xml (the Galaxy tool definition)
-
-The suggested location is the tools/sr_assembly folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool and also do
-this to tools_conf.xml.sample in order to run any tests:
-
-<tool file="sr_assembly/seq_primer_clip.xml" />
-
-You will also need to install MIRA, we used version 3.2.1. See:
-
-http://chevreux.org/projects_mira.html
-http://sourceforge.net/projects/mira-assembler/
-
-WARNING: This tool was developed to construct viral genome assembly and
-mapping pipelines, for which the run time and memory requirements are
-negligible. For larger tasks, be aware that MIRA can require vast amounts
-of RAM and run-times of over a week are possible. This tool wrapper makes
-no attempt to spot and reject such large jobs.
-
-
-History
-=======
-
-v0.0.1 - Initial version (working prototype)
-v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-tar -czf mira_wrapper.tar.gz tools/sr_assembly/mira.*
-
-Check this worked:
-
-$ tar -tzf mira_wrapper.tar.gz
-tools/sr_assembly/mira.py
-tools/sr_assembly/mira.txt
-tools/sr_assembly/mira.xml
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
--- a/mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.xml	Thu Jun 16 04:44:00 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,131 +0,0 @@
-<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.2">
-    <description>Takes Sanger, Roche, and Illumina data</description>
-	<command interpreter="python">mira.py mira $out_fasta $out_qual $out_tcs $out_ace $out_caf $out_wig $out_log
-##Give the wrapper script list of output filenames, then the mira command...
-mira --job=$job_method,$job_type,$job_quality
-
-##Input files
-#if $condBackbone.use == "true":
-    ## Can this be linked to job_method as well? If mapping we need the backbone...
-    -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename}
-#end if
-#if $condSanger.use == "true":
-    Sanger_SETTINGS
-    ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead
-    -LR:lsd=yes
-    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
-    -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename}
-#end if
-#if $condRoche.use == "true":
-    454_SETTINGS
-    ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead
-    -LR:lsd=yes
-    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
-    -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename}
-#end if
-#if $condIllumina.use == "true":
-    SOLEXA_SETTINGS
-    ## Not easy to add solexa to --job, so use load_sequence_data(lsd) instead
-    -LR:lsd=yes -LR:ft=fastq -FN:fgi=${condIllumina.filename}
-    ##TODO - Look at -LR FASTQ qual offset (fqqo)
-#end if
-
-
-##Output files
-COMMON_SETTINGS
-##remove_rollover_logs, remove_log_directory
--OUT:rrol=yes -OUT:rld=yes
-
-    </command>
-	<inputs>
-        <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
-            <option value="denovo">De novo</option>
-            <option value="mapping">Mapping</option>
-        </param>
-        <param name="job_type" type="select" label="Assembly type">
-            <option value="genome">Genome</option>
-            <option value="est">EST (transcriptome)</option>
-        </param>
-        <param name="job_quality" type="select" label="Assembly quality grade">
-            <option value="normal">Normal</option>
-            <option value="draft">Draft</option>
-            <option value="accurate">Accurate</option>
-        </param>
-        <!-- Backbone -->
-        <conditional name="condBackbone">
-           <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
-              <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
-           </when>
-        </conditional>
-        <!-- Sanger -->
-        <conditional name="condSanger">
-           <param name="use" type="select" label="Sanger/Capillary reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
-           </when>
-        </conditional>
-        <!-- Roche 454 -->
-        <conditional name="condRoche">
-           <param name="use" type="select" label="454 reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq,sff" label="Roche 454 reads file" help="FASTQ format" />
-           </when>
-        </conditional>
-        <!-- Illumina -->
-        <conditional name="condIllumina">
-           <param name="use" type="select" label="Solexa/Illumina reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
-           </when>
-        </conditional>
-	</inputs>
-	<outputs>
-	    <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
-	    <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
-	    <data name="out_tcs" format="tabular" label="MIRA contigs summary" />
-	    <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
-	    <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
-	    <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
-	    <data name="out_log" format="txt" label="MIRA log" />
-    </outputs>
-	<tests>
-	</tests>
-	<requirements>
-		<requirement type="python-module">Bio</requirement>
-	</requirements>
-	<help>
-
-**What it does**
-
-Runs MIRA v3, collects the output, and throws away all the temporary files.
-
-The MIRA transposed contig summary (TCS) file is converted into a tabular file for use within Galaxy.
-This records one line per base per contig, and including things like the base, quality, coverage and any tags.
-
-**Citation**
-
-This tool uses MIRA. If you use this tool in scientific work leading to a
-publication, please cite:
-
-Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
-
-	</help>
-</tool>